Introduction

This plugin enables you to mutate any residue of a PDB structure into one of the non-natural L- or D-sidechains of the SwissSidechain database.

If you do not have PyMOL, it can be obtained here.

The SwissSidechain PyMOL plugin was enhanced by Thomas Holder, Schrodinger Inc., for Python 3 compatibility and user-frendly installation.
This new version of the plugin is compatible with all PyMOL versions since PyMOL 1.5.0.6 (released in 2012).
We recommend the installation of this new version. However, the previous one is still available here.

Installation

• Download file PySwissSidechain2.zip.
• Install PySwissSidechain2.zip with the plugin manager.
• Finish the installation with "Plugin > Legacy Plugins > PySwissSidechain install fragments".

Running

Plugin Menu (on Mac,version 1.0 to 1.4)

Go under the Plugin->PySwissSidechain:

• Enter the residue you want to mutate as: Object//Chain/ResNumber/ (e.g., complex//E/82/)
• Enter the new residue code (e.g., HLEU)

Command line

Use the command:

  Mutate Object//Chain/ResNumber/, Newres

For instance, to mutate residue number '82' on chain 'E' in object 'complex' into Homoleucine (HLEU), write:

  Mutate complex//E/82/, HLEU

You can then choose between the different rotamers by clicking on the arrows at the lower right corner (same as standard Mutagenesis). Click 'Apply' and 'Done' to validate your mutation.

If you only have one object, you can simply write:

  Mutate Chain/ResNumber/, Newres

D-amino acids

Use the Pymol plugin D_PySwissSidechain.zip.

Instal it in the same way as the PySwissSidechain plugin.

The plugin appears under Plugin->D_PySwissSidechain.
The command line uses 'D_Mutate' instead of 'Mutate'.